mtDNA-Server 2 is a Nextflow DSL2 pipeline to accurately detect heteroplasmic and homoplasmic variants in mitochondrial (mtDNA) genomes, details can be found in our NAR publication.
The documentation can be accessed here.
Weissensteiner H*, Forer L*, Kronenberg F, Schönherr S. mtDNA-Server 2: advancing mitochondrial DNA analysis through highly parallelized data processing and interactive analytics. Nucleic Acids Res. 2024 May 6:gkae296. doi: 10.1093/nar/gkae296. Epub ahead of print. PMID: 38709886.
Release v2.1.15 - Add option for min mean coverage
Release v2.1.14 - Load resource conf
Release v2.1.13 - Update to latest Haplogrep3
Release v2.1.12 - Install Haplogrep3 tree directly.
Release v2.1.11 - Improve QC command, update to latest mutserve v2.0.1.
Release v2.1.10 - Improved mutect2 support: create missing RG tags, write inidividual reference sequence on the fly, support complex ref tags.
Ticket: INC20738179
- Error message:
Failed to pull singularity image - Root cause/issue: the container build was initiated on a node not configured for container building
- Solution Provided: instructions for
- Building Containers
- Update the pipeline configuration to use the local image
- Run the pipeline with the test profile
Note: the nextflow.config file has been updated to configure the pipeline to submit each task as a separate job.
Requirements
- The required container has been locally built and is saved in a "containers" folder - as described in the ticket
- The small input data file (
sample_S.bam) has been downloaded to the working directory (same location as the main.nf)
Here are the commands for running the pipeline on the SCC:
cd /projectnb/ar-rcs/client/nmf35/INC20738179_Nextflow/aramp10_fork/mtdna-server-2
module load nextflow/25.04.7
# Submit each task as a job:
nextflow run main.nf -profile test,singularity -c mtdna-server-2.config
# Run the pipeline locally:
nextflow run main.nf -profile test,singularity -c mtdna-server-2.config -process.executor local